Bio::AnnotationI(3pm) | User Contributed Perl Documentation | Bio::AnnotationI(3pm) |
Bio::AnnotationI - Annotation interface
# generally you get AnnotationI's from AnnotationCollectionI's foreach $key ( $ac->get_all_annotation_keys() ) { @values = $ac->get_Annotations($key); foreach $value ( @values ) { # value is an Bio::AnnotationI, and defines a "as_text" method print "Annotation ",$key," stringified value ",$value->as_text,"\n"; # you can also use a generic hash_tree method for getting # stuff out say into XML format $hash_tree = $value->hash_tree(); } }
Interface all annotations must support. There are two things that each annotation has to support.
$annotation->as_text()
Annotations have to support an "as_text" method. This should be a single text string, without newlines representing the annotation, mainly for human readability. It is not aimed at being able to store/represent the annotation.
The second method allows annotations to at least attempt to represent themselves as pure data for storage/display/whatever. The method hash_tree should return an anonymous hash with "XML-like" formatting:
$hash = $annotation->hash_tree();
The formatting is as follows.
(1) For each key in the hash, if the value is a reference'd array - (2) For each element of the array if the value is a object - Assume the object has the method "hash_tree"; (3) else if the value is a reference to a hash Recurse again from point (1) (4) else Assume the value is a scalar, and handle it directly as text (5) else (if not an array) apply rules 2,3 and 4 to value
The XML path in tags is represented by the keys taken in the hashes. When arrays are encountered they are all present in the path level of this tag
This is a pretty "natural" representation of an object tree in an XML style, without forcing everything to inherit off some super-generic interface for representing things in the hash.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : as_text Usage : Function: single text string, without newlines representing the annotation, mainly for human readability. It is not aimed at being able to store/represent the annotation. Example : Returns : a string Args : none
Title : display_text Usage : my $str = $ann->display_text(); Function: returns a string. Unlike as_text(), this method returns a string formatted as would be expected for the specific implementation. Implementations should allow passing a callback as an argument which allows custom text generation; the callback will be passed the current implementation. Note that this is meant to be used as a simple representation of the annotation data but probably shouldn't be used in cases where more complex comparisons are needed or where data is stored. Example : Returns : a string Args : [optional] callback
Title : hash_tree Usage : Function: should return an anonymous hash with "XML-like" formatting Example : Returns : a hash reference Args : none
Title : tagname Usage : $obj->tagname($newval) Function: Get/set the tagname for this annotation value. Setting this is optional. If set, it obviates the need to provide a tag to Bio::AnnotationCollectionI when adding this object. When obtaining an AnnotationI object from the collection, the collection will set the value to the tag under which it was stored unless the object has a tag stored already. Example : Returns : value of tagname (a scalar) Args : new value (a scalar, optional)
2018-10-27 | perl v5.26.2 |